Research workbench
Crystal structure of heparinase II
Analyse Crystal structure of heparinase II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FUQ
- Type
- protein
- Length
- 1,494 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heparinase II protein
- Ligands
- MAN, GCU, XYS, RAM, ZN, PO4
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Heparinase II protein | protein | 747 | 30% helix, 26% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- GCU · alpha-D-glucopyranuronic acid · sugar · 2 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · 2 copies
- RAM · alpha-L-rhamnopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- FMT · Formic acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.75 | 0.79 | 82 | empty |
| 2 | 694 | 0.72 | 0.78 | 75 | empty |
| 3 | 504 | 0.64 | 0.76 | 40 | empty |
| 4 | 220 | 0.56 | 0.78 | 21 | MAN, RAM |
| 5 | 203 | 0.55 | 0.78 | 20 | RAM |
Interfaces
1 interface between chains.
- A–B · 1434 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan, 2 modified (O-glycosylation, cyclization).
Compared structures
- 2FUQ · Crystal Structure of Heparinase II · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 2FUQ · PDBe 2FUQ
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